Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Trp63

Cell type

Cell type Class
Lung
Cell type
Lung basal cells
NA
NA

Attributes by original data submitter

Sample

source_name
Post-flu lung basal cells
cell type
Post-flu lung basal cells
genotype
Np63 WT
treatment
DMSO
time
48h
chip antibody
rabbit anti-p63a (Cell Signaling, clone D2K8X)

Sequenced DNA Library

library_name
GSM6659481
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the SimpleChIP® Plus Enzymatic Chromatic IP with Magnetic Beads Kit (Cell Signaling) protocol according to manufacturers instructions. In short, after 48h in either DMSO or 1μM 4OHT, media was removed and monolayers were cross-linked for 20 minutes in 1% PFA. Following fixation quenching with glycine and pelleting, nuclei were isolated, treated with micrococcal nuclease, and sonicated four times for 15 seconds each with an ultrasonic sonicator with a 1/8-inch probe on ice to shear chromatin into 150bp-900bp fragments. 5ug of cross-linked, digested chromatin was immunoprecipitated using 1ug of either rabbit anti-p63α (Cell Signaling, clone D2K8X), rabbit anti-H3K27ac (Cell Signaling, clone D5E4), or rabbit anti-H3K27me3 (Cell Signaling, clone C36B11). ChIP-seq libraries were prepared using using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions. After library cleanup, library concentrations were quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and size validated on a TapeStation (Agilent Technologies).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
28131095
Reads aligned (%)
79.5
Duplicates removed (%)
19.7
Number of peaks
203 (qval < 1E-05)

mm9

Number of total reads
28131095
Reads aligned (%)
79.5
Duplicates removed (%)
19.7
Number of peaks
170 (qval < 1E-05)

Base call quality data from DBCLS SRA